I'm having the same issue with one of my models.. normally rendering engines are unable to render more then one layer of transparency.. its very commonly seen.
although most rendering engines have a way of rendering the layers in passes, so that they render correctly. however it doesn't seem that MMD has such a system in place
however I noticed that the PMD editor lets you re-order the materials.. this seems to also effect the rendering order of each material.. and somewhat fixed the problem I had.
the solution to this is being able to use 2bit alpha blend on some materials.. but I'm unable to find a way to force that.
so I guess we're just stuck with re-ordering of the materials :\
before:
http://i55.tinypic.com/34ih4qv.jpg
re-ordered materials:
http://i54.tinypic.com/2m5ntbk.jpg
material isolation:
http://i53.tinypic.com/2h7ozle.jpg
..material isolation is an old trick, which doesnt really solve the problem. if anyone knows how to use 2bit alpha blending in MMD, please let me know.
thanks
-mariokart64n